PDB Chemical Component AFG

The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.

Bond Distances for AFG

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P   1.610
OP3 HOP3   0.967
P OP1   1.480
P OP2   1.610
P O5'   1.610
OP2 HOP2   0.968
O5' C5'   1.429
N9 C4   1.372
N9 C8   1.368
N9 C1'   1.465
C4 N3   1.338
C4 C5   1.398
N3 C2   1.315
C2 N2   1.372
C2 N1   1.363
N2 HN21   0.970
N2 HN22   0.970
N1 C6   1.352
N1 HN1   0.970
C6 O6   1.219
C6 C5   1.413
C5 N7   1.359
N7 C8   1.309
C8 N29   1.384
C31 C32   1.391
C31 C36   1.378
C31 H31   1.080
C32 C33   1.391
C32 N29   1.396
C33 C34   1.377
C33 H33   1.080
C34 C35   1.394
C34 C37   1.510
C35 C36   1.397
C35 C39   1.484
C36 H36   1.080
C37 C38   1.508
C37 H371   1.090
C37 H372   1.090
C38 C39   1.392
C38 C40   1.380
C39 C43   1.396
C40 C41   1.384
C40 H40   1.079
C41 C42   1.383
C41 H41   1.080
C42 C43   1.380
C42 H42   1.080
C43 H43   1.080
N29 H29   0.970
C2' C1'   1.545
C2' C3'   1.545
C2' H2'   1.091
C2' H2''   1.090
C5' C4'   1.530
C5' H5'   1.090
C5' H5''   1.090
C4' O4'   1.445
C4' C3'   1.545
C4' H4'   1.090
O4' C1'   1.445
C1' H1'   1.090
C3' O3'   1.430
C3' H3'   1.090
O3' HO3'   0.966

Bond Angles for AFG

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P OP3 HOP3   114.0
OP3 P OP1   109.5
OP3 P OP2   109.5
OP3 P O5'   109.5
OP1 P OP2   109.5
OP1 P O5'   109.5
OP2 P O5'   109.5
P OP2 HOP2   114.0
P O5' C5'   123.0
O5' C5' C4'   109.4
O5' C5' H5'   109.5
O5' C5' H5''   109.5
C4 N9 C8   107.5
C4 N9 C1'   126.2
N9 C4 N3   134.1
N9 C4 C5   106.2
C8 N9 C1'   126.3
N9 C8 N7   109.6
N9 C8 N29   125.2
N9 C1' C2'   110.4
N9 C1' O4'   110.4
N9 C1' H1'   110.4
N3 C4 C5   119.7
C4 N3 C2   121.1
C4 C5 C6   118.7
C4 C5 N7   107.4
N3 C2 N2   119.1
N3 C2 N1   121.8
N2 C2 N1   119.1
C2 N2 HN21   120.0
C2 N2 HN22   120.0
C2 N1 C6   120.4
C2 N1 HN1   119.8
HN21 N2 HN22   120.0
C6 N1 HN1   119.8
N1 C6 O6   120.8
N1 C6 C5   118.3
O6 C6 C5   120.9
C6 C5 N7   133.9
C5 N7 C8   109.2
N7 C8 N29   125.2
C8 N29 C32   120.0
C8 N29 H29   120.0
C32 C31 C36   120.2
C32 C31 H31   119.9
C31 C32 C33   119.9
C31 C32 N29   120.0
C36 C31 H31   119.9
C31 C36 C35   120.1
C31 C36 H36   120.0
C33 C32 N29   120.1
C32 C33 C34   120.0
C32 C33 H33   120.0
C32 N29 H29   120.0
C34 C33 H33   120.0
C33 C34 C35   120.4
C33 C34 C37   132.1
C35 C34 C37   107.5
C34 C35 C36   119.5
C34 C35 C39   109.4
C34 C37 C38   106.0
C34 C37 H371   110.1
C34 C37 H372   110.1
C36 C35 C39   131.1
C35 C36 H36   119.9
C35 C39 C38   109.5
C35 C39 C43   131.1
C38 C37 H371   110.2
C38 C37 H372   110.2
C37 C38 C39   107.6
C37 C38 C40   132.1
H371 C37 H372   110.2
C39 C38 C40   120.3
C38 C39 C43   119.4
C38 C40 C41   120.0
C38 C40 H40   120.0
C39 C43 C42   119.9
C39 C43 H43   120.1
C41 C40 H40   120.0
C40 C41 C42   120.1
C40 C41 H41   120.0
C42 C41 H41   119.9
C41 C42 C43   120.2
C41 C42 H42   119.9
C43 C42 H42   119.9
C42 C43 H43   120.0
C1' C2' C3'   104.1
C1' C2' H2'   110.5
C1' C2' H2''   110.4
C2' C1' O4'   104.8
C2' C1' H1'   110.4
C3' C2' H2'   110.6
C3' C2' H2''   110.5
C2' C3' C4'   104.1
C2' C3' O3'   110.4
C2' C3' H3'   110.5
H2' C2' H2''   110.6
C4' C5' H5'   109.5
C4' C5' H5''   109.5
C5' C4' O4'   110.4
C5' C4' C3'   110.4
C5' C4' H4'   110.4
H5' C5' H5''   109.5
O4' C4' C3'   104.8
O4' C4' H4'   110.3
C4' O4' C1'   105.3
C3' C4' H4'   110.4
C4' C3' O3'   110.5
C4' C3' H3'   110.6
O4' C1' H1'   110.4
O3' C3' H3'   110.5
C3' O3' HO3'   114.1

Torsion Angles for AFG

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2   240.0
OP1 P OP3 O5'   120.0
OP2 P OP3 O5'   240.0
OP3 P OP2 HOP2   60.0
OP3 P O5' C5'   175.0
HOP3 OP3 P OP1   299.9
HOP3 OP3 P OP2   59.9
HOP3 OP3 P O5'   179.9
OP1 P OP3 HOP3   299.9
OP3 P OP1 OP2   120.0
OP3 P OP1 O5'   240.0
OP2 P OP1 O5'   120.0
OP1 P OP2 HOP2   180.0
OP1 P O5' C5'   55.0
OP2 P OP3 HOP3   59.9
OP3 P OP2 OP1   240.0
OP3 P OP2 O5'   120.0
OP1 P OP2 O5'   240.0
OP2 P O5' C5'   295.0
O5' P OP3 HOP3   179.9
OP3 P O5' OP1   120.0
OP3 P O5' OP2   240.0
OP1 P O5' OP2   120.0
O5' P OP2 HOP2   300.0
P O5' C5' C4'   180.0
P O5' C5' H5'   300.0
P O5' C5' H5''   60.0
HOP2 OP2 P O5'   300.0
C4' C5' O5' H5'   240.0
C4' C5' O5' H5''   120.0
O5' C5' C4' O4'   66.5
O5' C5' C4' C3'   181.8
O5' C5' C4' H4'   304.2
H5' C5' O5' H5''   240.0
C8 N9 C4 C1'   180.3
C4 N9 C8 N7   360.0
C4 N9 C8 N29   179.9
C4 N9 C1' C2'   105.1
C4 N9 C1' O4'   220.5
C4 N9 C1' H1'   342.8
N3 C4 N9 C5   179.9
N9 C4 N3 C2   180.0
N9 C4 C5 C6   180.0
N9 C4 C5 N7   359.9
C4 N9 C8 C1'   179.7
C8 N9 C4 N3   180.0
C8 N9 C4 C5   0.1
C8 N9 C1' C2'   284.7
C8 N9 C1' O4'   40.1
C8 N9 C1' H1'   162.4
C5 N7 C8 N9   360.0
N7 C8 N9 N29   180.1
N9 C8 N29 C32   185.2
N9 C8 N29 H29   5.2
C4 N9 C1' C8   180.4
C1' N9 C4 N3   359.7
C1' N9 C4 C5   179.7
C1' N9 C8 N7   180.3
C1' N9 C8 N29   0.2
N9 C1' C2' C3'   142.8
N9 C1' C2' H2'   261.5
N9 C1' C2' H2''   24.1
C2' C1' N9 O4'   244.6
C2' C1' N9 H1'   122.3
C4' O4' C1' N9   200.7
O4' C1' N9 H1'   237.7
N3 C4 N9 C8   180.0
N3 C4 N9 C1'   359.7
N9 C4 N3 C5   180.1
N3 C4 C5 C6   0.0
N3 C4 C5 N7   180.0
C4 N3 C2 N2   180.0
C4 N3 C2 N1   360.0
C5 C4 N9 C8   0.1
C5 C4 N9 C1'   179.7
N9 C4 C5 N3   180.0
C5 C4 N3 C2   360.0
N1 C6 C5 C4   0.0
O6 C6 C5 C4   180.0
C6 C5 C4 N7   180.0
C4 C5 N7 C8   0.0
C2 N3 C4 C5   360.0
N2 C2 N3 N1   180.0
N3 C2 N2 HN21   0.0
N3 C2 N2 HN22   180.0
N3 C2 N1 C6   0.0
N3 C2 N1 HN1   180.0
N3 C2 N2 N1   180.0
N2 C2 N1 C6   180.1
N2 C2 N1 HN1   0.0
HN21 N2 C2 HN22   180.0
N3 C2 N1 N2   180.0
N1 C2 N2 HN21   180.0
N1 C2 N2 HN22   360.0
C6 N1 C2 HN1   180.1
C2 N1 C6 O6   180.0
C2 N1 C6 C5   359.9
HN21 N2 C2 N1   180.0
C2 N2 HN21 HN22   180.0
HN22 N2 C2 N1   360.0
C2 N2 HN22 HN21   180.0
C4 C5 C6 N1   0.0
C2 N1 C6 HN1   179.9
O6 C6 N1 C5   180.1
N1 C6 C5 N7   180.1
C2 N1 HN1 C6   180.1
HN1 N1 C6 O6   0.1
HN1 N1 C6 C5   180.0
C4 C5 C6 O6   180.0
O6 C6 N1 HN1   0.1
N1 C6 O6 C5   179.9
O6 C6 C5 N7   0.0
C4 C5 C6 N7   180.0
C5 C6 N1 HN1   180.0
N1 C6 C5 O6   180.1
C6 C5 N7 C8   180.0
N9 C8 N7 C5   360.0
C4 C5 N7 C6   180.0
C5 N7 C8 N29   180.1
N7 C8 N9 C1'   180.3
N9 C8 N7 N29   179.9
N7 C8 N29 C32   5.1
N7 C8 N29 H29   185.2
N29 C8 N9 C1'   0.2
N9 C8 N29 N7   180.1
C31 C32 N29 C8   210.0
C33 C32 N29 C8   30.0
C32 N29 C8 H29   180.0
C8 N29 C32 C31   210.0
C36 C31 C32 H31   180.3
C32 C31 C36 C35   360.0
C32 C31 C36 H36   180.0
C33 C32 C31 N29   180.0
C31 C32 C33 C34   0.1
C31 C32 C33 H33   179.9
C31 C32 N29 H29   30.0
C32 C31 C36 H31   179.7
C36 C31 C32 C33   360.0
C36 C31 C32 N29   180.0
C34 C35 C36 C31   360.0
C31 C36 C35 C39   180.0
C35 C36 C31 H36   180.0
C32 C31 H31 C36   180.3
H31 C31 C32 C33   179.7
H31 C31 C32 N29   359.7
H31 C31 C36 C35   180.3
H31 C31 C36 H36   0.3
C8 N29 C32 C33   30.0
C33 C32 C31 C36   360.0
C33 C32 C31 H31   179.7
C31 C32 C33 N29   180.0
C33 C32 N29 H29   210.0
C34 C33 C32 H33   180.1
C32 C33 C34 C35   359.9
C32 C33 C34 C37   180.0
C8 N29 C32 H29   180.0
N29 C32 C31 C36   180.0
N29 C32 C31 H31   359.7
C31 C32 N29 C33   180.0
N29 C32 C33 C34   180.1
N29 C32 C33 H33   359.9
C34 C33 C32 N29   180.1
C32 C33 C34 H33   179.9
C35 C34 C33 C37   179.9
C33 C34 C35 C36   0.0
C33 C34 C35 C39   180.0
C33 C34 C37 C38   180.0
C33 C34 C37 H371   299.1
C33 C34 C37 H372   60.8
H33 C33 C32 N29   359.9
C32 C33 H33 C34   180.1
H33 C33 C34 C35   180.1
H33 C33 C34 C37   0.1
C31 C36 C35 C34   360.0
C35 C34 C33 H33   180.1
C33 C34 C35 C37   180.1
C35 C34 C37 C38   0.0
C35 C34 C37 H371   119.2
C35 C34 C37 H372   240.9
C36 C35 C34 C39   180.0
C34 C35 C36 H36   180.0
C34 C35 C39 C38   360.0
C34 C35 C39 C43   180.0
C37 C34 C33 H33   0.1
C33 C34 C37 C35   179.9
C37 C34 C35 C36   180.0
C37 C34 C35 C39   360.0
C38 C37 C34 H371   240.9
C38 C37 C34 H372   119.2
C34 C37 C38 C39   359.9
C34 C37 C38 C40   180.0
H371 C37 C34 H372   238.3
C35 C36 C31 H31   180.3
C31 C36 C35 H36   180.0
C36 C35 C34 C37   180.0
C34 C35 C36 C39   180.0
C36 C35 C39 C38   180.0
C36 C35 C39 C43   0.0
C39 C35 C34 C37   360.0
C34 C35 C39 C36   180.0
C39 C35 C36 H36   360.0
C37 C38 C39 C35   0.0
C35 C39 C38 C40   180.0
C38 C39 C35 C43   180.0
C35 C39 C43 C42   179.9
C35 C39 C43 H43   360.0
H36 C36 C31 H31   0.3
C31 C36 H36 C35   180.0
H36 C36 C35 C39   360.0
C34 C37 C38 H371   119.1
C34 C37 C38 H372   240.9
C35 C39 C38 C37   0.0
H371 C37 C38 H372   121.8
C39 C38 C37 C40   179.9
C37 C38 C39 C43   180.0
C37 C38 C40 C41   180.0
C37 C38 C40 H40   359.9
C34 C37 H371 C38   243.4
C34 C37 H371 H372   121.7
C38 C37 H371 H372   238.2
H371 C37 C38 C39   240.9
H371 C37 C38 C40   61.0
C34 C37 H372 C38   116.6
C34 C37 H372 H371   238.4
C38 C37 H372 H371   121.8
H372 C37 C38 C39   119.1
H372 C37 C38 C40   299.2
C35 C39 C38 C43   180.0
C39 C38 C37 H371   240.9
C39 C38 C37 H372   119.1
C37 C38 C39 C40   180.1
C39 C38 C40 C41   0.1
C39 C38 C40 H40   180.0
C38 C39 C43 C42   360.0
C38 C39 C43 H43   180.0
C40 C38 C37 H371   61.0
C40 C38 C37 H372   299.2
C37 C38 C40 C39   179.9
C40 C38 C39 C43   359.9
C41 C40 C38 H40   180.1
C38 C40 C41 C42   0.0
C38 C40 C41 H41   180.0
C35 C39 C43 C38   180.0
C43 C39 C38 C40   359.9
C41 C42 C43 C39   0.1
C39 C43 C42 H42   180.0
C42 C43 C39 H43   179.9
C38 C40 C41 H40   179.9
C42 C41 C40 H41   180.0
C40 C41 C42 C43   359.9
C40 C41 C42 H42   180.0
C38 C40 H40 C41   180.1
H40 C40 C41 C42   180.1
H40 C40 C41 H41   0.0
C39 C43 C42 C41   0.1
C42 C41 C40 H40   180.1
C40 C41 C42 H41   180.0
C43 C42 C41 H42   179.9
C41 C42 C43 H43   180.1
H41 C41 C40 H40   0.0
C40 C41 H41 C42   180.0
H41 C41 C42 C43   179.9
H41 C41 C42 H42   0.0
C39 C43 C42 H43   180.1
C43 C42 C41 H41   179.9
C41 C42 C43 H42   180.1
H42 C42 C41 H41   0.0
C41 C42 H42 C43   179.9
H42 C42 C43 H43   360.0
C39 C43 H43 C42   179.9
H43 C43 C42 H42   360.0
C8 N29 H29 C32   180.0
N9 C1' C2' O4'   118.8
N9 C1' C2' H1'   237.7
C3' C2' C1' H2'   241.3
C3' C2' C1' H2''   118.6
C1' C2' C3' C4'   0.0
C1' C2' C3' O3'   118.7
C1' C2' C3' H3'   241.3
H2' C2' C1' H2''   237.4
C4' O4' C1' C2'   319.5
O4' C1' C2' H1'   118.9
C1' C2' C3' H2'   118.6
C1' C2' C3' H2''   241.4
C3' C2' C1' O4'   23.9
C3' C2' C1' H1'   265.1
H2' C2' C3' H2''   122.8
C5' C4' C3' C2'   217.2
O4' C4' C3' C2'   336.0
C2' C3' C4' H4'   94.8
C4' C3' C2' O3'   241.3
C4' C3' C2' H3'   118.7
O3' C3' C2' H3'   237.4
C2' C3' O3' HO3'   61.5
C1' C2' H2' C3'   245.3
C1' C2' H2' H2''   122.6
H2' C2' C1' O4'   142.6
H2' C2' C1' H1'   23.8
C3' C2' H2' H2''   237.2
H2' C2' C3' C4'   241.4
H2' C2' C3' O3'   0.0
H2' C2' C3' H3'   122.7
C1' C2' H2'' C3'   114.6
C1' C2' H2'' H2'   237.4
H2'' C2' C1' O4'   265.3
H2'' C2' C1' H1'   146.4
C3' C2' H2'' H2'   122.8
H2'' C2' C3' C4'   118.6
H2'' C2' C3' O3'   237.3
H2'' C2' C3' H3'   359.9
O5' C5' C4' H5'   120.0
O5' C5' C4' H5''   240.0
C2' C3' C4' C5'   217.2
H5' C5' C4' H5''   120.0
O4' C4' C5' C3'   244.6
O4' C4' C5' H4'   122.3
C5' C4' O4' C1'   159.3
C3' C4' C5' H4'   237.6
C5' C4' C3' O3'   98.6
C5' C4' C3' H3'   335.8
O5' C5' H5' C4'   240.0
O5' C5' H5' H5''   120.0
C4' C5' H5' H5''   240.0
H5' C5' C4' O4'   306.5
H5' C5' C4' C3'   61.8
H5' C5' C4' H4'   184.2
O5' C5' H5'' C4'   120.0
O5' C5' H5'' H5'   240.0
C4' C5' H5'' H5'   120.0
H5'' C5' C4' O4'   186.5
H5'' C5' C4' C3'   301.8
H5'' C5' C4' H4'   64.2
N9 C1' O4' C4'   200.7
C2' C1' O4' C4'   319.5
C2' C3' C4' O4'   336.0
O4' C4' C5' H5'   306.5
O4' C4' C5' H5''   186.5
C5' C4' O4' C3'   118.8
C5' C4' O4' H4'   237.7
C3' C4' O4' H4'   118.9
O4' C4' C3' O3'   217.4
O4' C4' C3' H3'   94.7
C4' O4' C1' H1'   78.4
C4' C3' C2' H2'   241.4
C4' C3' C2' H2''   118.6
C2' C3' C4' O3'   118.6
C2' C3' C4' H3'   241.3
C3' C4' C5' H5'   61.8
C3' C4' C5' H5''   301.8
C5' C4' C3' O4'   241.1
C5' C4' C3' H4'   122.3
O4' C4' C3' H4'   241.2
C3' C4' O4' C1'   40.5
O3' C3' C4' H3'   122.7
C4' C3' O3' HO3'   176.1
H4' C4' C5' H5'   184.2
H4' C4' C5' H5''   64.2
C5' C4' H4' O4'   122.3
C5' C4' H4' C3'   237.7
O4' C4' H4' C3'   115.4
H4' C4' O4' C1'   281.6
H4' C4' C3' O3'   336.2
H4' C4' C3' H3'   213.5
N9 C1' O4' C2'   241.1
N9 C1' O4' H1'   122.3
O4' C1' C2' C3'   23.9
O4' C1' C2' H2'   142.6
O4' C1' C2' H2''   265.3
C2' C1' O4' H1'   241.2
C1' O4' C4' C3'   40.5
C1' O4' C4' H4'   281.6
N9 C1' H1' C2'   122.3
N9 C1' H1' O4'   237.7
H1' C1' C2' C3'   265.1
H1' C1' C2' H2'   23.8
H1' C1' C2' H2''   146.4
C2' C1' H1' O4'   115.4
O3' C3' C2' H2'   0.0
O3' C3' C2' H2''   237.3
C2' C3' O3' C4'   245.3
C2' C3' O3' H3'   122.6
O3' C3' C4' H4'   336.2
C4' C3' O3' H3'   237.3
H3' C3' C2' H2'   122.7
H3' C3' C2' H2''   359.9
C2' C3' H3' C4'   114.7
C2' C3' H3' O3'   237.4
H3' C3' C4' H4'   213.5
C4' C3' H3' O3'   122.7
H3' C3' O3' HO3'   298.9
HO3' O3' C3' H3'   298.9